On Tue, Mar 29, 2011 at 2:17 PM, Douglas Bates <ba...@stat.wisc.edu> wrote: > On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung > <ht...@users.sourceforge.net> wrote: >> Martin Maechler wrote: >>>>>>>> >>>>>>>> Douglas Bates <ba...@stat.wisc.edu> >>>>>>>> on Mon, 28 Mar 2011 09:24:39 -0500 writes: >>> >>> > Can you provide the output from sessionInfo() >>> >>> > so we can know the platform? Also, did you configure R >>> > with --enable-strict-barrier or set the C compilation flag >>> > -DTESTING_WRITE_BARRIER? I think that run-time error >>> > message can only be thrown under those circumstances (not >>> > that it isn't an error, it's just not checked for in other >>> > circumstances). >>> >>> interesting. >>> >>> In the mean time, I *did* run --- for several hours! --- >>> your code example below, >>> and it did *not* segfault for me (64-bit, Linux Fedora 13). >>> >>> Martin >> >> 64-bit fedora 14. For building R svn (and checking soon-to-be-released R >> packages, rather than daily R-related work), I also have these, and indeed >> have "--enable-strict-barrier": >> >> export DEFS='-DUSE_TYPE_CHECKING_STRICT -DR_MEMORY_PROFILING' \ >> ./configure --enable-memory-profiling --enable-strict-barrier >> --enable-byte-compiled-packages --with-valgrind-instrumentation=2 >> >>> sessionInfo() >> R version 2.14.0 Under development (unstable) (--) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base > > Thanks for the information. I can replicate the problem on a Red Hat > EL 5 64-bit system and will start to debug now.
I isolated the problem and tested then committed a fix. I am going to ask Martin to upload the new release as I have gotten out of sync with some of his recent changes and he will, I hope, reconcile the branches and trunk. If you need the fixed version immediately, say for testing, the changes are in the file Matrix/src/chm_common.c You can visit the SVN archive for the project, https://r-forge.r-project.org/scm/?group_id=61, click on the link to Browse Subversion Repository and go to pkg/Matrix/src/chm_common.c I made the mistake that I chastised others for making, performing an operation on the result of a call to install and another value that may have required allocation of memory. The first time install is called on a particular string it allocates and SEXPREC, which may cause a garbage collection. >>>>>>>> Douglas Bates <ba...@stat.wisc.edu> >>>>>>>> on Mon, 28 Mar 2011 09:24:39 -0500 writes: >>> >>> > Can you provide the output from >>> > sessionInfo() >>> >>> > so we can know the platform? Also, did you configure R with >>> > --enable-strict-barrier or set the C compilation flag >>> > -DTESTING_WRITE_BARRIER? I think that run-time error message can >>> only >>> > be thrown under those circumstances (not that it isn't an error, it's >>> > just not checked for in other circumstances). >>> >>> > On Sat, Mar 26, 2011 at 5:21 PM, Hin-Tak Leung >>> <hintak_le...@yahoo.co.uk> wrote: >>> >> Current core/Recommended Matrix package (0.999375-48) has been >>> segfaulting against R 2.13-alpha/2.14-trunk for the last week or so (since >>> R-2.13 was branched, when I started trying) when "run with R CMD check >>> --use-gct": >>> >> >> -------------- >>> >>> pkgname <- "Matrix" >>> >>> source(file.path(R.home("share"), "R", "examples-header.R")) >>> >>> gctorture(TRUE) >>> >>> options(warn = 1) >>> >>> library('Matrix') >>> >> Loading required package: lattice >>> >> Error : .onLoad failed in loadNamespace() for 'Matrix', details: >>> >> call: fun(...) >>> >> error: unprotected object (0x2768b18) encountered (was REALSXP) >>> >> Error: package/namespace load failed for 'Matrix' >>> >> Execution halted >>> >> --------------- >>> >> >> I traced to this because "R CMD check --use-gct snpStats" >>> (both 1.1.13 and 1.1.12) segfaults with the same message, and before that, >>> the snpMatrix 1.15.8.4 which includes some of David's newly written ld() ( >>> which depends on Matrix.) >>> >> >> If the Matrix package segfaults, David's new ld() isn't >>> useable. >>> >> >> >> > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel